Naruto Magica
by Crookedknuckle86
Summary: Homura Akemi is unwillingly transported into the world of Shinobi. In a world where Kyubey doesn't seem to exist, will Homura be able to find Madoka and finally get things right this time around? [This story is under reconstruction right now, please bear with me!]
1. Chapter 1 REDONE

**Hi! Thank you for all the kind words and encouragement! I have decided that I want to fix up this story, so please bear with me. If any of the events in this chapter seem confusing, please let me know so I can do my best to explain/fix it. Reviews are always appreciated, and as always: I do not own either of these franchises. Naruto and Madoka Magica do not belong to me.**

 _Is this a dream?_ Homura wondered. She was no longer in her bedroom. Instead, she was somewhere that resembled outer space. _Something's not right here_ , she thought.

"Homura Akemi." Homura quickly turned her head toward the sound.

"Incubator," she responded coldly.

"It seems that your power grants you the ability to travel between timelines, so it makes sense that you would be able to travel between realities as very interesting," Kyubey continued.

"Between realities?" Homura paused. She had not reset the timeline again, so why would reality be changing? "What are you playing at, Incubator?"

"You are no longer the only magical girl to have wished to change reality in such a drastic way."

"What do you mean?" She asked. Something was very wrong, and she feared it would make it all that much harder to save Madoka.

"My newest contract made a wish to change reality so that it matches that of the shinobi world. I am not entirely sure what the shinobi world is, but the contract _was_ completed."

Homura vaguely remembered reading a manga with shinobi in it back when she was still in the hospital. _What was it called… Naruto?_ She wondered. However, she had not read much of it. She had started the series just a few weeks prior to attending Mitakihara. She had quickly lost interest in the concept when she discovered the existence of magical girls. Seeing that there were people with real powers fighting all around her made the whole concept seem very boring and almost insulting, in a way.

"That's insane! Why would someone trade their soul just to poke around in some story?"

"That is none of my concern. She will eventually turn into a witch regardless of what she wished for."

"What was the exact wording of her wish?" Homura asked with a mix of curiosity and trepidation.

"She wished that everyone who fights witches be transported into the shinobi world."

Homura was so focused on trying to figure out the nature of this wish that one could practically see the gears turning in her head. _People who fight wishes were not necessarily magical girls. Technically speaking, anyone who has helped a magical girl fight would be included in this… reality jump…_ "Which means that Madoka is affected," Homura finished aloud.

Kyubey simply nodded, confirming her suspicions.

"However…" She continued as her violet eyes stared intensely into red ones, "Couldn't it be said, Incubator, that your ultimate goal is to create witches, and not to fight them?" Although Kyubey's face remained as impassive as ever, it was easy to tell that the same conclusion Homura had come to. "And couldn't it be said that because of this, you are not actually included in this wish? It would have been wise to think of this before you granted such a request," Homura said with what could only be a smirk.

For a creature with no emotions, Kyubey sure seemed pissed.

...

Homura awoke to find that she was in a bed that was not her own. _The dream I had last night was definitely real. However, I have no idea where I landed within this universe._ Surveying the apartment she was in, Homura looked for signs of where and who she was within the shinobi world. However, she found that it was more useful to notice what she did _not_ have. She rummaged through all the drawers there, but did not find any weapons or battle-ready clothing. From what she could tell, Homura was a civilian and not a shinobi. _Good_ , thought Homura, _It will be easier for me to find Madoka if I don't have anyone I have to report back to._ The other thing that was lacking was any sort of identification, or even just photos of family and friends. _It seems that even here, I'm alone. The lack of identification papers for myself could be a problem… I'll have to figure out a solution for that soon, especially if I need to leave the area. Speaking of, what area exactly am I talking about?_

Although Homura had thoroughly inspected what was presumably her apartment, she still did not know what village or even what nation she was in. After putting on the plain black tee shirt, gray pants and blue sandals, Homura felt that she could blend right in with a crowd. _Just the look I'm going for_ , she mused. Feeling confident she wouldn't draw attention to herself, Homura then grabbed some of the money she had found in her dresser and walked out of her apartment into the new world around her.

Figuring that she was going to end up doing at least a little traveling in search of Madoka, Homura decided that it would be a good idea to stock up on supplies for the road.

While she wasn't normally one to invade other people's privacy, Homura needed all the information she could get. So while she was shopping, she made it a point to eavesdrop on the people surrounding her. Most of what she heard wasn't all that useful, however, she eventually landed on a conversation of much interest.

"Did you see where that medic with the pink hair went? I was hoping I could get the chance to thank her before she left," she heard a woman ask her friend.

"She took off along the main road a few hours ago. She seemed to be in quite the hurry to get back before the afternoon," another woman replied. "I wish she had stuck around a little longer, I didn't even catch her name."

 _Pink haired medic? Could it be her? Kohona sounds like less than a day's journey. If I hurry, I can make it there before sunset, especially with my abilities. It's not much to go on, but it's a start._

...

After a long day of walking, Homura had finally made it to Konoha. She was almost in view of the main gate when she heard a shout.

"You have to let me in!" The voice exclaimed. "I swear I'm just here to buy a few things! I'm just civilian!"

Another person responded, presumably whoever was guarding the entrance. "No papers, no entry. Simple as that."

 _Well, shit. I'm not going to be able to get in without some kind of ID, and I can only stop time for so long. If I go to the hospital to look for that pink haired medic, I'm going to have to be able to talk to her. If I just appear out of nowhere and start talking, there's no way I won't get attacked for being an intruder. Besides, even if it_ is _Madoka in there, I'm not going to be able to stay for long if I'm not supposed to be there._

The only option was for Homura to be brought willingly into Konoha, or better yet for Homura to be brought into the hospital.

 _If I appear to have a life threatening injury, They'll bring me in for treatment. Even better, I can fake amnesia once I get there. That way it won't look too suspicious when I have no explanation for who I am or what I'm doing in Konoha._

Homura knew that the guards at the gate were most likely ninja, and would therefore be able to tell a real injury from a fake one. That meant that her seemingly life threatening injury would have to actually be life threatening to a civilian. _Good thing I'm not a civilian_ , Homura mused to herself, although in reality she definitely wasn't looking forward to what she was about to do.

After checking her surroundings to make sure no one would see her, she summoned her shield. Time had to be stopped while doing this or else someone might hear. Reluctantly, Homura turned her shield and watch the world meld into shades of gray.

Luckily for her, Homura had learned how to block out pain completely long ago. While it was dangerous to do in battle, it was definitely a useful skill to have in other situations. Of the things she remembered from the Naruto manga, they didn't have guns in this world. _If I use a gun for this, it'll look very suspicious, seeing as guns don't exist here._

She fished around in her arsenal, looking for something that wasn't a gun or bomb. After much digging, she found an old golf club from her early days as a magical girl, as well as a pocket knife she kept in there for convenience purposes. _Not my witch hunting gear, but it'll work for what I have in mind. Besides, I can always heal myself up later._

After she had heavily injured herself, Homura decided it would be a good idea to tear a few holes in her clothing to really make it look convincing. She lowered her shield and let time start again, and then started staggering to the gate. For once in her life, Homura was grateful that her consciousness was separate from her body. While she didn't have a mirror to see what she looked like, she knew she had done quite a bit of damage, which would cause quite a bit of pain if she had to feel it. As she got closer to the gate, she made sure to let out a few groans, and overall have a look of extreme pain on her face. Homura knew she wasn't the best actor, but she hoped it would be enough to get her inside.

Once the guards began shouting and running toward her, Homura stumbled to the ground, pretending to fall unconscious.

...

When Homura regained consciousness, she found that she was laying in a hospital bed. _Wait. Why am I waking up? When did I_ actually _lose consciousness? That wasn't supposed to happen!_

Homura's thought's were quickly interrupted, however, when her eyes landed on the other person in the room. As they turned towards her, Homura was surprised to see she recognized the face. It was not who she was looking for, but Homura still felt a sense of relief as her eyes met with a pair of all-too-familiar blue ones **.**

 **Well, That covers what I had written up to this point. As you can see, I've changed some of the basic plot, mainly the fact that Kyubey is no longer in the picture. Does my writing for that make sense? Reviews are always very appreciated!**


	2. Chapter 2

**Hi! This took a lot longer than expected, thank you for being so patient with me. Before I forget, I wanted to mention that this story takes shortly before Shippuden does. Sakura has been training with Tsunade and all that, but Naruto hasn't returned home. For Homura, this is somewhere near the middle of her series of time loops. So without further adieu, here's the next little piece of the story.**

 **UPDATE: I reposted this chapter because the link in email notifications wasn't working.**

 **.…**

Sayaka Miki stood over the hospital bed, peering into the violet eyes of Homura Akemi.

"Now that you're awake, maybe you can answer some questions for me," Sayaka said inquisitively.

"Such as?" Homura asked coyly. Homura had expected this of course. She was, after all, a stranger in the center of a country's military city.

"Well for starters, mind telling me who you are?"

Homura paused for a moment before answering, feigning a struggle to remember. "...Homura Akemi," she answered with false uncertainty.

"What exactly were you doing where you wound up outside of Konoha, bruised and bleeding? That doesn't exactly sound like you're a 'friendly civilian', if you ask me," Sayaka said somewhat nonchalantly.

As Homura watched Sayaka fold her arms, she noticed something peculiar. Sayaka's ring was absent from her finger. _She's not wearing her soul gem, but she definitely contracted in the last timeline._ However, she caught a glimpse of something else on Sayaka's hands. Strange symbols covered her palms. _Some sort of seal?_ Sayaka stared at Homura, awaiting a response. Homura frowned. "You mentioned Konoha. Is that where we are?"

" are in Konoha hospital," Sayaka responded. However, the fact that Homura blatantly dodged her question did not go unnoticed.

"How did I get here? And why did I need to go to the hospital?" Homura asked.

"Beats me. That's why I asked you, remember?" Sayaka asked, her voice laced with irritation. "All we know is that you wandered in here half dead. It took us hours just to fix you up." Sayaka chose to leave out how unusual Homura's body seemed. While Homura was being healed, it became apparent that her chakra pathways had never been used. However, she was strong and fit in a way that was unheard of for anyone who wasn't a ninja. _And a high level one too_ , thought Sayaka. _Something just isn't adding up,_ Sayaka thought to herself.

Homura tentatively opened her mouth to speak, only to be silenced by the sight of a bright pink head of hair passing by the doorway. Before she could stop herself, she uttered a single word. "Madoka."

In the blink of an eye, Sayaka had a sword to her throat. Where it had come from, Homura had no idea. _Maybe it has something to do with the seals I saw earlier,_ she mused.

The fact that Homura seemed completely unphased by a weapon pointed directly at one of her vital points was more than a little concerning to Sayaka. _Okay, definitely a red flag_ , Sayaka thought. "Where have you heard that name before?" Sayaka hissed, trying to sound as intimidating as possible.

"What name? I didn't say anything"

" _Bullshit."_

 _Uh-oh._ Now Sayaka was livid. Things usually got out of hand once she started losing control of her emotions. Having noticed Sayaka's outburst, the pink haired girl turned around. "Sayaka, what's going on?" the girl asked, already on guard.

 _Shit. Definitely not Madoka._ The girl in front of her shared her hair color, but not much else. Madoka had pink eyes that matched her hair, but the person in front of her had leaf green eyes with a glare that managed to unsettle even Homura. Her face was more slender, and was definitely a little older than Madoka, although it couldn't have been by more than a couple of years. Rather than red ribbons, she wore a red headband with a metal leaf insignia on it. Paired with her muscular body, it was obvious the girl was a ninja. _She seems pretty familiar, I know she was in the story before. What was her name again? Sakura?_

"She knows something about Madoka." _And since we haven't seen her since she and all those other genin were taken by Orochimaru, this Homura chick has to be connected to him._

 _It seems I wasn't too far off coming here, even if my initial reasons proved to not be true,_ Homura thought, eyeing the pink haired medic she had tracked here.

Sayaka shared a glance with Sakura(?) to confirm that they had come to the same conclusion. The harsh determination in her eyes suggested that she had.

"She seemed pretty suspicious from the start, considering how she just appeared out of nowhere," Sakura remarked.

"She was probably gonna head to interrogation at some point anyways, so we might as well speed up that process."

 _Interrogation? As much as I want to find out what these two know about Madoka, I don't have an alibi or actual backstory I can use here._

And before the two ninja could even notice what she was doing, Homura had summoned her shield and time stopped. Homura jumped out the window, headed for a place to hide until she could come up with a plan B. As she ran, she tried to decide if she would better off leaving town or trying to blend in as a civilian. _My soul gem is getting too dark to keep this time stop up for too much longer. If I want to keep going, I need to stop and clean my soul gem._

Right on cue, her shield clicked and time was no longer paused. _I can't keep time stopped for long stretches right now. I need to find somewhere to stop._

They hadn't even so much as blinked and their patient had disappeared. Making a dash for the window which had mysteriously been opened, Sayaka looked down at the road in front of them, watching Homura run down the street while seemingly blinking in and out of existence. Sayaka called out for Sakura, who had been checking the hallway for their missing patient. After gaining her attention, Sayaka gestured to the window before jumping out. Sakura followed close behind, ready to chase their newfound lead on their missing Madoka.

…

"And just where do you think you're going?"

Sayaka was evidently a lot faster here than she ever was in Mitakihara, based on how she had just caught up to Homura from a fairly long distance away. Having received no response (save for a glare) from Homura, Sayaka continued.

"We're not letting you get away that easy. Not until you tell us what you know about Madoka."

 _What_ I _know? Why do they need to know about Madoka?_ Despite her confusion, Homura remained silent, simply intensifying her stare.

"If you're not going to cooperate, I'm just gonna have to drag you to interrogation by force." And with that, Sayaka put her hands together and made a motion for a seal. She then brought her her hands apart, a line of swords hitting the ground as she did so. _So i was correct to assume that those were seals on her hands. It seems her powers managed to translate over to this universe. I wonder if her healing abilities came with her._

Just like back in Mitakihara, Sayaka was picking up the swords and whipping them Homura's way. Wanting to preserve her magic, Homura thought it best to avoid stopping time as of right now. She managed to dodge them, but not quite fast enough to avoid a nick or two. Not sure if she should bring out the big guns yet, Homura stuck to dodging attacks until she could formulate a plan. For now, she stayed in civilian clothes, not wanting to reveal her transformation abilities. She already had her shield out, so she had lost her element of surprise in that it was definitely easier to fight and maintain magic while fully transformed, suddenly changing her entire outfit in the blink of an eye might be the final mark of suspicious things against her. For now, Homura would just have to keep avoiding getting impaled by airborne swords.

Seeing as Homura had pretty much been able to avoid her long range attacks, Sayaka had switched to direct swordplay. As of right now, Homura was using her old golf club to block the sword being swung at her. Although Homura was proficient enough at fighting, Sayaka was definitely faring better in this fight. The golf club wasn't really meant to be used as a weapon, so the attacks were damaging to it. A couple more blows and the club would probably break. On top of that, Sword fighting was not Homura's area of expertise by any means. Sayaka, however, had plenty of experience. _If I don't start using real weapons, I'm not going to win this. But will Sayaka be okay if I use a gun? Maybe I should just knock her out. But how would Sakura react to that? Speaking of which, where_ is _she? I thought she would've showed up to help Sayaka by now._ Looking out into the distance, Homura tried to quickly scan for signs of Sakura. Sure enough, she could see a pink head of hair getting pretty close.

That minor distraction on Homura's part was all Sayaka needed to get the advantage. With a powerful swing of her arm, she landed a direct hit on Homura's club. And with that, the golf club snapped in half. Immediately, Sayaka jabbed her with the blunt end of her sword (also not wanting to heavily injure), causing Homura to double over. Seizing the moment of vulnerability, Sayaka hit Homura at the base of her neck, rendering her unconscious. Right on cue, Sakura finally caught up to help carry her to interrogation.

 **…**

 **Wow! I am actually the worst at updating! Anyways, do you see where I'm going with this? I know the plot is a little weird, but I'm just writing for fun/practice so hopefully y'all don't mind it too much. Madoka's missing and Sayaka, Sakura, and Homura all want to find her?Hmm… Maybe we'll see some teamwork in the future? Also: In this fanfiction, Madohomu is canon, but this isn't a Madohomu fic. The relationship is more a motivating factor than an actual plot point (if that makes any sense). As always, reviews are very much appreciated. Thanks for reading!**


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